Re: spontaneous system explosion after 2 ns of normal run

From: Jian Liu (
Date: Mon Oct 19 2009 - 01:45:24 CDT

Hello Roman and others paying attention to this problem:

I have ran into a same problem as yours.
My system was built in various modelling softwares,
  and the charges in water moleclues was confused somewhere.
It returned to normal after be corrected.

Hoping can help you

Jian Liu
Master-degree graduate candidate majoring in Molecular Modelling
Department of Physical Chemistry \& Chemical Physics
College of Chemistry, Chemical Engineering and Materials Science
Soochow University
Suzhou 215123, China
----- Original Message -----
From: Roman Petrenko <>
To: NAMD list <>
Subject: namd-l: spontaneous system explosion after 2 ns of normal run
Date: 2009-10-15 11:57:34
Dear namd-ers,

i simulated a protein system inserted in membrane in a water box with

ions (total charge is close to zero) with PBC. Box size 159x159x112 A.

NPT ensemble with electric field (of 1 namdconf unit) perpendicular to

membrane was applied. Simulation runs normally up to 1,000,000 steps

(2 ns) with normal decrease in total energy, temperature and pressures

correspond to target values. Only slight increase in water box (by a

couple of angstroms) was observed.

Then, during the following 1.4 ns the box size increases to

5190x5190x3650 A and visually everything explodes.

In other runs with exactly the same system but 10 times smaller

electric field 4.4 ns of simulations are as expected.

Should it explode when 10 ns is reached? Has anyone observed system

explosion _after_ the system is minimized and partially equilibrated?


Roman Petrenko

Physics Department

University of Cincinnati

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